Despite the high sensitivity and relatively high tolerance for contaminants of matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry (MALDI‐TOF MS) there is often a need to purify and concentrate the sample solution, especially after in‐gel digestion of proteins separated by two‐dimensional gel electrophoresis (2‐DE). A silicon microextraction chip (SMEC) for sample clean‐up and trace enrichment of peptides was manufactured and investigated. The microchip structure was used to trap reversed‐phase chromatography media (POROS™ R2 beads) that facilitates sample purification/enrichment of contaminated and dilute samples prior to the MALDI‐TOF MS analysis. The validity of the SMEC sample preparation technique was successfully investigated by performing analysis on a 10 nM peptide mixture containing 2 M urea in 0.1 M phosphate‐buffered saline with MALDI‐TOF MS. It is demonstrated that the microchip sample clean‐up and enrichment of peptides can facilitate identification of proteins from 2‐DE separations. The microchip structure was also used to trap beads immobilized with trypsin, thereby effectively becoming a microreactor for enzymatic digestion of proteins. This microreactor was used to generate a peptide map from a 100 nM bovine serum albumin sample.